subMaldi

subMALDI is an open framework package for the R programming environment that permits organization, pre-processing (smoothing, baseline correction, peak detection), and normalization of spectral data sets. As a result of the package's design, subMALDI data objects are compatible with functions from a wide variety of other R packages, and user-defined functions are easier to implement and test.

Installing in R

To install this package in R, begin by downloading the source copy of the package from the releases folder and install it using type = "source". But, before you do this, a dependency from the BioConductor project is required. Begin by installing the BioConductor Manager:

install.packages("BiocManager")

and then install the package MassSpecWavelet:

BiocManager::install("MassSpecWavelet")

Then install the CRAN-supported packages required:

install.packages(c("tidyr", "ggplot2", "ggpmisc", "reshape2", "RColorBrewer", "signal"))

Once the packages are all installed, you can then install the package:

install.packages("subMALDI-1.0-2.tar.gz", type = "source")

Update the file name as necessary to whatever the copy you downloaded was set to for versioning.

Note: if you install from source, and set dependencies = TRUE, this should all be moot. This assumes you run the commands exactly as given, in which case, the BioConductor sequence doesn't always seem to work. For example,

install.packages("subMALDI-1.0-2.tar.gz", type = "source", dependencies = TRUE)

Getting Started

Refer to the vignette on workflow for a brief summary of the package functionality, and the vignette on processing for a simple example.

Contributing?

Examine our contribution guidelines for more.